Dear Prayagraj,
averaging a MD trajectory will most often produce distorted structures.
A better approach for the identification of the most important
conformations is clustering, which yields 'reasonable' structures, i.e.
cluster representatives.
See the Amber manual on cpptraj for more details and examples.
Regards,
Anselm
Am 27.06.2016 12:52, schrieb Prayagraj Fandilolu:
> Hi everyone,
>
>
>
> I am analysing a MD trajectory for average and snapshot structures using
> cpptraj.
>
>
>
> I have performed 50ns of MD with the following parameters. There are total
> 2500 frames in my trajectory.
>
>
>
> ntx=1, irest=0, ntpr=1000, ntwx=10000, ntwr=100000,
>
> ntf=2, ntb=2, cut=9.0, nsnb=10,
>
> ntr=0,
>
> imin=0, nstlim=25000000, dt=0.002
>
>
>
> I am using following average.in script for calculating the average
> structure.
>
> /
>
> trajin md.crd
>
> average 2180-2500.pdb pdb start 2180 stop 2500 .1-66
>
> strip:WAT
>
> /
>
>
>
> The pdb which I get after processing shows much more overlapped and
> distorted structure.
>
>
>
> I want to calculate the averages over frames 2180-2500 (nearly 40-50ns) in
> batches of 5 or 10 frames per structure and also the overall average
> structure.
>
>
>
> What input should I design so as to get clear average structures with no
> distortions?
>
>
>
> Thanks in advance!!!!!
>
>
>
> Mr. Prayagraj Fandilolu
> Research Scholar,
> Structural Bioinformatics Unit
> Department of Biochemistry
> Shivaji University, Kolhapur - 416004
> (MS) India
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jun 27 2016 - 05:00:02 PDT
